Human Immunodeficiency Virus Type 1 Population Genetics and Adaptation in Newly Infected Individuals

• DOI: 10.1128/jvi.01960-08
• Publication Date: 2008-12-31T01:25:57Z
• Authors: M. Kearney; F. Maldarelli; W. Shao; J. B. Margolick; E. S. Daar; J. W. Mellors; V. Rao; J. M. Coffin; S. Palmer
• Keywords: Nonsynonymous substitution; CTL*

Studies on human immunodeficiency virus type 1 (HIV-1) diversity are critical for understanding viral pathogenesis and the emergence of immune escape variants design vaccine strategies. To investigate HIV-1 population genetics, we used single-genome sequencing to obtain pro-pol env sequences from longitudinal samples (n = 93) 14 acutely or recently infected patients. The first available sample after infection 12/14 patients revealed populations with low genetic diversity, consistent transmission outgrowth a single variant. In contrast, two showed high coexistence distinct in collected days nonreactive enzyme-linked immunosorbent assay indeterminate Western blot, multiple variants. Comparison PR RT all consensus subgroup B sequence that nearly nonsynonymous differences were confined identified cytotoxic T-lymphocyte (CTL) epitopes. For HLA-typed patients, mutations compared transmitted found epitopes would not be recognized by patient's major histocompatibility complex type. Reversion was rarely seen over study interval (up 5 years). These data indicate acute subtype usually results carrying CTL selected prior either donor previous reversion these can very slow. have important implications strategies because they imply some HLA alleles could compromised newly acquired HIV infections.